5MOG

Oryza sativa phytoene desaturase inhibited by norflurazon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation.

Brausemann, A.Gemmecker, S.Koschmieder, J.Ghisla, S.Beyer, P.Einsle, O.

(2017) Structure 25: 1222-1232.e3

  • DOI: 10.1016/j.str.2017.06.002

  • PubMed Abstract: 
  • Cyanobacteria and plants synthesize carotenoids via a poly-cis pathway starting with phytoene, a membrane-bound C40 hydrocarbon. Phytoene desaturase (PDS) introduces two double bonds and concomitantly isomerizes two neighboring double bonds from tran ...

    Cyanobacteria and plants synthesize carotenoids via a poly-cis pathway starting with phytoene, a membrane-bound C40 hydrocarbon. Phytoene desaturase (PDS) introduces two double bonds and concomitantly isomerizes two neighboring double bonds from trans to cis. PDS assembles into homo-tetramers that interact monotopically with membranes. A long hydrophobic tunnel is proposed to function in the sequential binding of phytoene and the electron acceptor plastoquinone. The herbicidal inhibitor norflurazon binds at a plastoquinone site thereby blocking reoxidation of FADred. Comparison with the sequence-dissimilar bacterial carotene desaturase CRTI reveals substantial similarities in the overall protein fold, defining both as members of the GR2 family of flavoproteins. However, the PDS active center architecture is unprecedented: no functional groups are found in the immediate flavin vicinity that might participate in dehydrogenation and isomerization. This suggests that the isoalloxazine moiety is sufficient for catalysis. Despite mechanistic differences, an ancient evolutionary relation of PDS and CRTI is apparent.


    Organizational Affiliation

    Institute for Biochemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phytoene dehydrogenase, chloroplastic/chromoplastic
A, B, C, D, E
497Oryza sativa subsp. indicaMutation(s): 0 
Gene Names: PDS1 (PDS)
EC: 1.3.5.5
Find proteins for A2XDA1 (Oryza sativa subsp. indica)
Go to UniProtKB:  A2XDA1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A, B, E
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NRF
Query on NRF

Download SDF File 
Download CCD File 
A, B, C, D, E
Norflurazon
C12 H9 Cl F3 N3 O
NVGOPFQZYCNLDU-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D, E
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B, D
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
B, D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.209 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 230.210α = 90.00
b = 230.210β = 90.00
c = 179.230γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
BUSTERrefinement
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Database references